Microelectrode oxygen profiles were measured in intertidal sediments from Ria Formosa (S. Portugal), a very productive shallow coastal lagoon. Four intertidal sampling sites were selected according to different sediment characteristics. Individual profiles revealed a high degree of lateral variability on a centimeter spatial scale. Nevertheless, consistent differences were observed between oxygen profiles measured in atmosphere-exposed and inundated intertidal sediments: in organically poor sand oxygen-penetration depth varied from 3 mm in inundated cores to more than 7 mm in exposed ones, while in organically rich muddy sand and mud it remained between 0.5–2.0 mm. The oxygen input from inundated to exposed conditions was estimated for each sampling site. Semi-diurnal tidal fluctuation, leading to periodical atmospheric exposure of sediments plays a major role in the oxygenation process of intertidal zones of Ria Formosa.